CRISPR screen

GENETHOFF: a flexible workflow for genome wide profiling of CRISPR/Cas off targets

GENETHOFF is a Snakemake workflow for analyzing CRISPR/Cas9 off-targets from GUIDE-Seq data, handling multiple organisms and Cas nucleases through a metadata-driven approach.

Engineering Synthetic Cell State Transitions by Harnessing Epigenetic Memory

This paper engineers synthetic epigenetic circuits that induce stable gene expression changes and drive cell state transitions through transient cell-cell interactions.

Epigenetic CRISPR Screening of 9p21.3 Non-Coding Regions identifies Cis-Regulatory Elements of P16INK4a and P15INK4b Controlling Cellular Senescence

The paper identifies cis-regulatory elements controlling cellular senescence by performing CRISPR screens in human mesenchymal stromal cells, revealing a primate-specific SINE element that modulates P16INK4a and P15INK4b.

Engineered Promoter System Enables High-efficiency Transgenic CRISPR Editing in Malaria Transmitting Mosquito Anopheles sinensis

The paper identifies effective promoters for CRISPR editing in Anopheles sinensis, achieving high editing efficiency in transgenic mosquitoes.

Directed evolution of a compact TranC11a system for efficient genome editing

This study evolves the TranC11a system to improve genome editing efficiency in human and plant cells, achieving performance comparable to SpCas9.

Multiplex base editing of BCL11A regulatory elements to treat sickle cell disease

This study uses multiplex base editing to target BCL11A enhancers, increasing fetal hemoglobin production and reducing sickle cell disease symptoms without causing significant genomic damage.

A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs

The paper constructs a co-essentiality network from CRISPR screens to prioritize anticancer targets and predict drug responses, outperforming conventional networks in drug repurposing.

Anti-cancer compound screening identifies Aurora Kinase A inhibition as a means to favor CRISPR/Cas9 gene correction over knock-out

This study screens cancer drugs to find those that enhance HDR over NHEJ in CRISPR gene editing, identifying Aurora kinase A inhibitors as promising candidates.

Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

The paper identifies disease-linked regulatory DNA variants and their impact on epidermal homeostasis by analyzing SNVs, TF binding, and gene dysregulation in polygenic skin diseases.

Efficient installation of heterozygous mutations in human pluripotent stem cells using prime editing

This study demonstrates the use of prime editing to efficiently introduce heterozygous mutations in human pluripotent stem cells with high knock-in efficiency and without purification or selection steps.

Genetically encoded RNA strand exchange circuits for programmable protein expression and computation in cells

This study demonstrates genetically encoded RNA strand exchange circuits in living cells, showing that in vitro TMSE design principles apply to E. coli but with cellular-specific caveats.

CRISPR-Cas12a REC2 - NUC interactions drive target-strand cleavage and constrain trans cleavage.

This study investigates differences in cis and trans cleavage efficiency among Cas12a orthologues and identifies REC2-NUC interactions as key determinants of their function.

An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates

The paper uses an image-based CRISPR screen to show splicing regulates HP1α condensates through RNA-chromatin interactions, affecting heterochromatin organization and stress response genes.

Investigation of Double-Stranded DNA Donors and CRISPR-Cas9 RNP for Universal Correction of Mutations Causing Cystic Fibrosis in Human Airway Cells

This study demonstrates that low levels of CFTR integration can restore chloride ion currents in human airway cells using optimized nonviral CRISPR-Cas9 RNP and double-stranded DNA donors.

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice

This study identifies four resistance mechanisms to sustained auxin-inducible protein degradation in human cells and mice using the AID2 system.

Pooled CRISPR screens identify genes and non-coding genomic regions that regulate red blood cell density

The paper uses CRISPR screens to identify genes and non-coding regions affecting red blood cell density, finding 17 genes and 13 regions, some novel, that regulate this trait.

Universal Single Copy Knock-In System in Caenorhabditis elegans: One Plasmid to Target All Chromosomes

The paper introduces a universal single-copy knock-in system for C. elegans that allows transgene insertion at specific loci using CRISPR/Cas9.

RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistance

RESTRICT-seq improves CRISPR screens by restricting Cas9 activity in time-gated cycles, revealing novel epigenetic drivers of cSCC resistance.

DNA damage hypersensitivity in chicken primordial germ cells limits CRISPR-Cas9 editing and supports an shRNA-based screening approach

The paper identifies DNA damage hypersensitivity in chicken PGCs as a barrier to CRISPR-Cas9 editing and demonstrates shRNA as a viable alternative for functional screening.

Engineered prime editors with minimal genomic errors

This paper designs prime editors with repositioned DNA breaks to significantly reduce indel errors while maintaining editing efficiency.

Rosace-AA: Enhancing Interpretation of Deep Mutational Scanning Data with Amino Acid Substitution and Position-Specific Insights

Characterization and engineering of highly efficient Cas12j genome editors

This study identifies and engineers novel Cas12j orthologues into efficient genome editors with enhanced editing activity and specific sequence requirements.

A systematic survey of distal element-gene regulatory interactions with Direct-Capture Targeted Perturb-seq

This study identifies most distal element-gene interactions have small effect sizes (<10%) using DC-TAP-seq, revealing limitations in prior CRISPR screens and suggesting new model requirements.

Repurposing base editors for targeted knock-in and simultaneous knockouts to generate multiplex-edited allogeneic CAR T cells with minimal translocations

This paper develops BEKI, a base editor-based method for targeted transgene insertion and multiplex gene disruption in T cells, reducing chromosomal translocations compared to Cas9-based approaches.

Systematic identification and characterization of regulators of aryl hydrocarbon receptor signaling

This study identifies regulators of AHR signaling in hepatocytes using CRISPR screening, revealing novel mechanisms and cell-type-specific components for therapeutic targeting.

A lectin-based magnetic CRISPR screening protocol permits rapid discovery of genes regulating cell-surface glycosylation

The paper introduces a lectin-based magnetic CRISPR screening protocol that enables faster and easier identification of genes regulating cell-surface glycosylation, applied to breast cancer hypersialylation.

SPACE: multimodal spatial CRISPR screening with whole-transcriptome readout at subcellular resolution in 3D models

SPACE enables spatial CRISPR screening with whole-transcriptome and protein readouts at subcellular resolution, revealing novel regulatory mechanisms in tumor microenvironments.

Coupling CRISPR Scanning with Targeted Chromatin Accessibility Profiling using a Double-Stranded DNA Deaminase

This paper introduces TDAC-seq, a method combining CRISPR perturbations with chromatin accessibility profiling to study cis-regulatory elements at single-nucleotide resolution.

Versatile and efficient non-viral integration of large transgenes in human T cells via CRISPR knock-in and engineered integrases

This paper introduces one-pot PASTA, a non-viral method for efficient large transgene integration in human T cells using CRISPR and integrases, showing improved performance over existing methods.

Pioneer factor FOXA1 can boost CHO cell productivity

This study shows that overexpressing the pioneer factor FOXA1 in CHO cells increases monoclonal antibody production by improving transgene promoter accessibility and transcription.